rebeccagarner/paleocapture

Scripts associated with the article "Sediment Metagenomes as Time Capsules of Lake Microbiomes"

Sediment Metagenomes as Time Capsules of Lake Microbiomes

Pipelines and scripts associated with the article

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Garner RE, Gregory-Eaves I, Walsh DA. 2020. Sediment Metagenomes as Time Capsules of Lake Microbiomes. mSphere 5:e00512-20. https://doi.org/10.1128/mSphere.00512-20.

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Scripts

1. 01_pipeline.md Bioinformatics pipeline that begins with raw metagenome reads, (1) trims the raw reads, (2) assembles metagenomes from the trimmed reads, and (3) maps trimmed reads to the metagenomes.
2. 02_rnagenes.R Identify scaffolds containing conserved genes (ribosomal RNA or transfer rRNA genes) and count reads mapped (after removing scaffolds containing conserved genes).
3. 03_idhist.R Read mapping vs. sequence identity in captured metagenomes.
4. 04_genecontent.R Calculate gene counts on scaffolds in free and captured metagenomes.
5. 05_covlength.R Scaffold coverage vs. length.
6. 06_taxonomy.R Taxonomic analyses of free and captured metagenomes.
7. 07_genera.R Gene counts for selected taxa in free metagenomes.
8. 08_virusphylogeny.R Identify genes encoding Caudovirales terminase large subunit.
9. 09_mapgenomes.R Map metagenome reads to reference reference genomes accessed from IMG.

Note on metagenome file names: Numeric codes sometimes stand in for lake names: Lac Paula 06-126, Eightmile Lake 17-054, Grand lac Touradi 17-067. Surface water metagenomes are named watercolumn, top sediment metagenomes top, and bottom sediment metagenomes bottom.